Package: ecostate 0.2.0
James T. Thorson
ecostate: State-Space Mass-Balance Model for Marine Ecosystems
Fits a state-space mass-balance model for marine ecosystems, which implements dynamics derived from 'Ecopath with Ecosim' <https://ecopath.org/> while fitting to time-series of fishery catch, biomass indices, age-composition samples, and weight-at-age data. Package 'ecostate' fits biological parameters (e.g., equilibrium mass) and measurement parameters (e.g., catchability coefficients) jointly with residual variation in process errors, and can include Bayesian priors for parameters.
Authors:
ecostate_0.2.0.tar.gz
ecostate_0.2.0.tar.gz(r-4.5-noble)ecostate_0.2.0.tar.gz(r-4.4-noble)
ecostate_0.2.0.tgz(r-4.4-emscripten)ecostate_0.2.0.tgz(r-4.3-emscripten)
ecostate.pdf |ecostate.html✨
ecostate/json (API)
NEWS
| # Install 'ecostate' in R: |
| install.packages('ecostate', repos = 'https://cloud.r-project.org') |
Bug tracker:https://github.com/james-thorson-noaa/ecostate/issues
Pkgdown site:https://james-thorson-noaa.github.io
- eastern_bering_sea - Eastern Bering Sea ecosystem data
- whitehouse_2021 - Full rpath inputs for eastern Bering Sea
Last updated 4 months agofrom:738a1d5566. Checks:3 OK. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 25 2025 |
| R-4.5-linux | OK | Mar 25 2025 |
| R-4.4-linux | OK | Mar 25 2025 |
Exports:abm3pc_sysadd_equilibriumcompute_nllcompute_tracerdBdtddirmultecostateecostate_controlode23plot_foodwebprint_ecoparsrk4sysstanza_settings
Dependencies:backportscheckmateclicodacolorspacecpp11fansifarverggnetworkggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnetworknlmepillarpkgconfigR6RColorBrewerRcppRcppEigenrlangRTMBscalessnastatnet.commontibbleTMButf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adams-Bashford-Moulton for system of equations | abm3pc_sys |
| Compute equilibrium values | add_equilibrium |
| Compute negative log-likelihood for EcoState model | compute_nll |
| Calculate tracers, e.g., trophic level | compute_tracer |
| Dynamics from EcoSim | dBdt |
| Dirichlet-multinomial | ddirmult |
| eastern Bering Sea ecosystem data | eastern_bering_sea |
| fit EcoState model | ecostate |
| Detailed control for ecostate structure | ecostate_control |
| Penrose-Moore pseudoinverse | ginv |
| Marginal log-likelihood | logLik.ecostate |
| Non-stiff (and stiff) ODE solvers | ode23 |
| Plot foodweb | plot_foodweb |
| Print EcoSim parameters | print_ecopars |
| Print fitted ecostate object | print.ecostate |
| Classical Runge-Kutta for system of equations | rk4sys |
| Detailed control for stanza structure | stanza_settings |
| Full rpath inputs for eastern Bering Sea | whitehouse_2021 |
